Starting phenix.real_space_refine
on Thu Jul  2 10:52:21 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7la4_23245/07_2026/7la4_23245.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7la4_23245/07_2026/7la4_23245.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7la4_23245/07_2026/7la4_23245.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7la4_23245/07_2026/7la4_23245.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7la4_23245/07_2026/7la4_23245.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7la4_23245/07_2026/7la4_23245.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7la4_23245/07_2026/7la4_23245.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7la4_23245/07_2026/7la4_23245.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     Mg      1      5.21       5
     S      33      5.16       5
     C    5213      2.51       5
     N    1386      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8281
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "H"
      Number of atoms: 911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 911
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
    Chain: "L"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 821
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103}
    Chain: "A"
      Number of atoms: 3467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3467
          Classifications: {'peptide': 452}
          Link IDs: {'PTRANS': 27, 'TRANS': 424}
    Chain: "B"
      Number of atoms: 2940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 2940
          Classifications: {'peptide': 377}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 357}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen chiralities: 4
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 18
          Unusual residues: {' CA': 4, 'NAG': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' MG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 1.90, per 1000 atoms: 0.23
  Number of scatterers: 8281
  At special positions: 0
  Unit cell: (102, 110, 100, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      6     19.99
     S      33     16.00
     Mg      1     11.99
     O    1642      8.00
     N    1386      7.00
     C    5213      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  56 " - pdb=" SG  CYS A  65 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 130 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 146 " - pdb=" SG  CYS A 167 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 177 " - pdb=" SG  CYS B 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 232 " - pdb=" SG  CYS B 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 374 " - pdb=" SG  CYS B 386 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " MAN D   3 " - " MAN D   4 "
    ALPHA1-4
      " NAG D   2 " - " MAN D   3 "
      " NAG E   2 " - " MAN E   3 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG A1105 " - " ASN A  15 "
      " NAG C   1 " - " ASN B  99 "
      " NAG D   1 " - " ASN B 320 "
      " NAG E   1 " - " ASN B 371 "
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 458.7 milliseconds
  

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1912

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 19 sheets defined
      11.6% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.940A  pdb=" N   SER H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.955A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.605A  pdb=" N   ASP L  82 " --> pdb=" O   GLU L  79 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ILE L  83 " --> pdb=" O   GLN L  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 79 through 83'
    Processing helix  chain 'A' and resid 151 through 156
      removed outlier: 3.575A  pdb=" N   TYR A 155 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 159
      No H-bonds generated for 'chain 'A' and resid 157 through 159'
    Processing helix  chain 'A' and resid 187 through 192
    Processing helix  chain 'A' and resid 200 through 205
    Processing helix  chain 'B' and resid 121 through 125
    Processing helix  chain 'B' and resid 130 through 134
    Processing helix  chain 'B' and resid 135 through 143
    Processing helix  chain 'B' and resid 170 through 175
      removed outlier: 4.058A  pdb=" N   GLU B 174 " --> pdb=" O   PRO B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 203
      removed outlier: 3.760A  pdb=" N   ARG B 202 " --> pdb=" O   GLN B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 232
      removed outlier: 3.889A  pdb=" N   ALA B 225 " --> pdb=" O   GLY B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 237
    Processing helix  chain 'B' and resid 259 through 264
      removed outlier: 3.794A  pdb=" N   LEU B 262 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 302
      removed outlier: 3.865A  pdb=" N   LYS B 298 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 322
      removed outlier: 3.775A  pdb=" N   ASN B 320 " --> pdb=" O   ASN B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 349
      removed outlier: 3.916A  pdb=" N   VAL B 345 " --> pdb=" O   LEU B 341 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 22 through 23
    Processing sheet with id=AA2, first strand: chain 'H' and resid 45 through 47
    Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 14
      removed outlier: 3.733A  pdb=" N   GLN L  89 " --> pdb=" O   ASN L  34 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 9 through 12
      removed outlier: 3.551A  pdb=" N   THR A   9 " --> pdb=" O   VAL A 447 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 23 through 27
    Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 77
      removed outlier: 3.502A  pdb=" N   PHE A  87 " --> pdb=" O   HIS A 112 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 97 through 99
    Processing sheet with id=AA9, first strand: chain 'A' and resid 116 through 117
      removed outlier: 3.738A  pdb=" N   GLU A 120 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 174 through 175
    Processing sheet with id=AB2, first strand: chain 'A' and resid 241 through 242
      removed outlier: 3.569A  pdb=" N   GLU A 252 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 256 through 257
      removed outlier: 6.323A  pdb=" N   VAL A 267 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   ARG A 279 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ILE A 269 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 293 through 295
      removed outlier: 3.535A  pdb=" N   VAL A 308 " --> pdb=" O   TYR A 329 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 314 through 315
    Processing sheet with id=AB6, first strand: chain 'A' and resid 360 through 362
      removed outlier: 3.691A  pdb=" N   GLN A 405 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 87 through 88
    Processing sheet with id=AB8, first strand: chain 'B' and resid 97 through 102
      removed outlier: 3.784A  pdb=" N   LYS B  98 " --> pdb=" O   ALA B 401 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA B 401 " --> pdb=" O   LYS B  98 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 97 through 102
      removed outlier: 3.784A  pdb=" N   LYS B  98 " --> pdb=" O   ALA B 401 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA B 401 " --> pdb=" O   LYS B  98 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 194 through 197
      removed outlier: 4.655A  pdb=" N   LEU B 196 " --> pdb=" O   ILE B 151 " (cutoff:3.500A)
      removed outlier: 5.811A  pdb=" N   ILE B 151 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   VAL B 112 " --> pdb=" O   ARG B 150 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   GLY B 152 " --> pdb=" O   VAL B 112 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ILE B 114 " --> pdb=" O   GLY B 152 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   GLY B 154 " --> pdb=" O   ILE B 114 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   TYR B 116 " --> pdb=" O   GLY B 154 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   PHE B 156 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   MET B 118 " --> pdb=" O   PHE B 156 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   VAL B 247 " --> pdb=" O   TYR B 115 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   THR B 250 " --> pdb=" O   ALA B 309 " (cutoff:3.500A)

    182 hydrogen bonds defined for protein.
    432 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.34

  Time building geometry restraints manager: 1.01 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 2701
        1.34 -     1.46: 1858
        1.46 -     1.58: 3847
        1.58 -     1.70: 0
        1.70 -     1.82: 49
  Bond restraints: 8455
  Sorted by residual:
  bond pdb=" N   ILE H  72 "
       pdb=" CA  ILE H  72 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.07e-02 8.73e+03 1.03e+01
  bond pdb=" N   TYR H 100 "
       pdb=" CA  TYR H 100 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.29e-02 6.01e+03 8.59e+00
  bond pdb=" N   ILE L 106 "
       pdb=" CA  ILE L 106 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.19e-02 7.06e+03 8.23e+00
  bond pdb=" N   ARG L  24 "
       pdb=" CA  ARG L  24 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.23e-02 6.61e+03 7.35e+00
  bond pdb=" N   ILE L  29 "
       pdb=" CA  ILE L  29 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.25e-02 6.40e+03 7.08e+00
  ... (remaining 8450 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 10666
        1.49 -     2.98: 677
        2.98 -     4.46: 108
        4.46 -     5.95: 23
        5.95 -     7.44: 12
  Bond angle restraints: 11486
  Sorted by residual:
  angle pdb=" N   PHE H 104 "
        pdb=" CA  PHE H 104 "
        pdb=" C   PHE H 104 "
      ideal   model   delta    sigma   weight residual
     111.71  105.39    6.32 1.34e+00 5.57e-01 2.23e+01
  angle pdb=" N   ASN L  31 "
        pdb=" CA  ASN L  31 "
        pdb=" C   ASN L  31 "
      ideal   model   delta    sigma   weight residual
     112.30  106.45    5.85 1.36e+00 5.41e-01 1.85e+01
  angle pdb=" N   VAL B 314 "
        pdb=" CA  VAL B 314 "
        pdb=" C   VAL B 314 "
      ideal   model   delta    sigma   weight residual
     113.20  109.15    4.05 9.60e-01 1.09e+00 1.78e+01
  angle pdb=" N   MET H  81 "
        pdb=" CA  MET H  81 "
        pdb=" C   MET H  81 "
      ideal   model   delta    sigma   weight residual
     114.64  108.32    6.32 1.52e+00 4.33e-01 1.73e+01
  angle pdb=" CA  ARG H  84 "
        pdb=" C   ARG H  84 "
        pdb=" O   ARG H  84 "
      ideal   model   delta    sigma   weight residual
     121.60  116.89    4.71 1.21e+00 6.83e-01 1.52e+01
  ... (remaining 11481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 4472
       17.99 -    35.98: 366
       35.98 -    53.98: 88
       53.98 -    71.97: 18
       71.97 -    89.96: 12
  Dihedral angle restraints: 4956
    sinusoidal: 1947
      harmonic: 3009
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.51   47.49     1      1.00e+01 1.00e-02 3.11e+01
  dihedral pdb=" CA  ASN B 377 "
           pdb=" C   ASN B 377 "
           pdb=" N   GLU B 378 "
           pdb=" CA  GLU B 378 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.33  -27.67     0      5.00e+00 4.00e-02 3.06e+01
  dihedral pdb=" CA  THR H  28 "
           pdb=" C   THR H  28 "
           pdb=" N   PHE H  29 "
           pdb=" CA  PHE H  29 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.47  -24.53     0      5.00e+00 4.00e-02 2.41e+01
  ... (remaining 4953 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 1242
       0.113 -    0.225: 44
       0.225 -    0.338: 5
       0.338 -    0.450: 0
       0.450 -    0.563: 1
  Chirality restraints: 1292
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN B  99 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.84   -0.56 2.00e-01 2.50e+01 7.93e+00
  chirality pdb=" CA  TYR H 106 "
            pdb=" N   TYR H 106 "
            pdb=" C   TYR H 106 "
            pdb=" CB  TYR H 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" CA  LEU A  84 "
            pdb=" N   LEU A  84 "
            pdb=" C   LEU A  84 "
            pdb=" CB  LEU A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.98e+00
  ... (remaining 1289 not shown)

  Planarity restraints: 1489
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 288 "   -0.026 2.00e-02 2.50e+03   1.85e-02 6.81e+00
        pdb=" CG  TYR A 288 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 288 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 288 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 288 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 288 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 288 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 288 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B  99 "   -0.024 2.00e-02 2.50e+03   2.24e-02 6.25e+00
        pdb=" CG  ASN B  99 "    0.028 2.00e-02 2.50e+03
        pdb=" OD1 ASN B  99 "   -0.006 2.00e-02 2.50e+03
        pdb=" ND2 ASN B  99 "    0.024 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  47 "   -0.013 2.00e-02 2.50e+03   1.44e-02 5.16e+00
        pdb=" CG  TRP H  47 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  47 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  47 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  47 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  47 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1486 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 244
        2.66 -     3.22: 8204
        3.22 -     3.78: 13004
        3.78 -     4.34: 18660
        4.34 -     4.90: 30829
  Nonbonded interactions: 70941
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 220 "
            pdb="MG    MG B2001 "
     model   vdw
     2.100 2.170
  nonbonded pdb=" OD1 ASN A 430 "
            pdb=" O   HOH A1201 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OH  TYR A 353 "
            pdb=" OE1 GLU B 297 "
     model   vdw
     2.138 3.040
  nonbonded pdb=" OG  SER A  22 "
            pdb=" O   GLY A  94 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" OE1 GLN A 197 "
            pdb=" OG  SER A 220 "
     model   vdw
     2.159 3.040
  ... (remaining 70936 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     9.380
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   8473  Z= 0.320
  Angle     :  0.853   7.438  11532  Z= 0.493
  Chirality :  0.056   0.563   1292
  Planarity :  0.004   0.043   1485
  Dihedral  : 14.950  89.960   3020
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 16.83
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  9.58 %
    Favored  : 89.94 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  2.70 %
    Favored  : 95.39 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.02 (0.24), residues: 1044
  helix: -3.78 (0.40), residues: 95
  sheet: -2.97 (0.25), residues: 351
  loop : -2.26 (0.24), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  41 
 TYR   0.044   0.002   TYR A 288 
 PHE   0.017   0.002   PHE B 370 
 TRP   0.037   0.003   TRP H  47 
 HIS   0.010   0.001   HIS A 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00597 /  0.32 ( 8455)
  covalent geometry    : angle       0.84387 /  0.49 (11486)
  SS BOND              : bond        0.00457 /  0.28 (    8)
  SS BOND              : angle       1.23502 /  0.70 (   16)
  hydrogen bonds       : bond        0.25976 / 17.40 (  178)
  hydrogen bonds       : angle      11.85270 /  7.95 (  432)
  link_ALPHA1-3        : bond        0.01013 /  0.53 (    1)
  link_ALPHA1-3        : angle       1.67376 /  0.96 (    3)
  link_ALPHA1-4        : bond        0.01025 /  0.50 (    2)
  link_ALPHA1-4        : angle       2.77565 /  1.45 (    6)
  link_BETA1-4         : bond        0.00639 /  0.31 (    3)
  link_BETA1-4         : angle       1.64593 /  0.83 (    9)
  link_NAG-ASN         : bond        0.00554 /  0.27 (    4)
  link_NAG-ASN         : angle       2.90592 /  1.87 (   12)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   26 SER cc_start: 0.7798 (p) cc_final: 0.7472 (t)
REVERT: A  232 ASP cc_start: 0.8234 (m-30) cc_final: 0.7997 (m-30)
  outliers start: 17
  outliers final: 2
  residues processed: 158
  average time/residue: 0.1011
  time to fit residues: 21.8175
Evaluate side-chains
  121 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain A residue   72 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  31 ASN
L  38 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.136405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.113146 restraints weight = 11545.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.84
r_work: 0.3237 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8473  Z= 0.176
  Angle     :  0.685   7.569  11532  Z= 0.349
  Chirality :  0.048   0.360   1292
  Planarity :  0.005   0.047   1485
  Dihedral  :  5.719  54.836   1151
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.58 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  9.89 %
    Favored  : 87.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.78 (0.24), residues: 1044
  helix: -3.50 (0.36), residues: 98
  sheet: -2.88 (0.24), residues: 368
  loop : -2.00 (0.25), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  41 
 TYR   0.029   0.002   TYR A 288 
 PHE   0.013   0.002   PHE B 308 
 TRP   0.015   0.002   TRP H  47 
 HIS   0.008   0.001   HIS A 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.18 ( 8455)
  covalent geometry    : angle       0.67607 /  0.35 (11486)
  SS BOND              : bond        0.00555 /  0.28 (    8)
  SS BOND              : angle       1.00661 /  0.54 (   16)
  hydrogen bonds       : bond        0.04438 /  2.99 (  178)
  hydrogen bonds       : angle       8.46868 /  5.56 (  432)
  link_ALPHA1-3        : bond        0.01406 /  0.74 (    1)
  link_ALPHA1-3        : angle       1.79718 /  0.99 (    3)
  link_ALPHA1-4        : bond        0.01249 /  0.60 (    2)
  link_ALPHA1-4        : angle       2.50385 /  1.35 (    6)
  link_BETA1-4         : bond        0.00308 /  0.16 (    3)
  link_BETA1-4         : angle       1.36515 /  0.69 (    9)
  link_NAG-ASN         : bond        0.00665 /  0.32 (    4)
  link_NAG-ASN         : angle       2.52613 /  1.64 (   12)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   61 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.8008 (mtm-85)
REVERT: A  270 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8054 (pp)
REVERT: A  285 MET cc_start: 0.8969 (mtp) cc_final: 0.8672 (mtm)
REVERT: B  259 ASP cc_start: 0.8106 (t70) cc_final: 0.7883 (t0)
  outliers start: 21
  outliers final: 8
  residues processed: 151
  average time/residue: 0.0965
  time to fit residues: 20.2160
Evaluate side-chains
  134 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain L residue   31 ASN
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  423 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 96 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0670
   chunk 77 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    1.5524

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L   6 GLN
L  27 GLN
L  31 ASN
L  38 GLN
L  92 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.132144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.105005 restraints weight = 11434.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.23
r_work: 0.3151 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   8473  Z= 0.272
  Angle     :  0.709   8.069  11532  Z= 0.358
  Chirality :  0.049   0.331   1292
  Planarity :  0.004   0.047   1485
  Dihedral  :  5.392  43.273   1149
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 10.06 %
    Favored  : 89.75 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 13.93 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.75 (0.24), residues: 1044
  helix: -3.36 (0.37), residues: 98
  sheet: -2.92 (0.24), residues: 369
  loop : -1.95 (0.25), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 147 
 TYR   0.035   0.002   TYR A 288 
 PHE   0.017   0.002   PHE B 308 
 TRP   0.014   0.002   TRP H  47 
 HIS   0.009   0.001   HIS A 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00637 /  0.27 ( 8455)
  covalent geometry    : angle       0.70044 /  0.36 (11486)
  SS BOND              : bond        0.00538 /  0.37 (    8)
  SS BOND              : angle       1.20445 /  0.66 (   16)
  hydrogen bonds       : bond        0.03991 /  2.68 (  178)
  hydrogen bonds       : angle       7.95484 /  5.18 (  432)
  link_ALPHA1-3        : bond        0.01324 /  0.70 (    1)
  link_ALPHA1-3        : angle       1.70882 /  0.95 (    3)
  link_ALPHA1-4        : bond        0.01395 /  0.68 (    2)
  link_ALPHA1-4        : angle       2.44204 /  1.32 (    6)
  link_BETA1-4         : bond        0.00244 /  0.12 (    3)
  link_BETA1-4         : angle       1.09938 /  0.58 (    9)
  link_NAG-ASN         : bond        0.00652 /  0.31 (    4)
  link_NAG-ASN         : angle       2.60321 /  1.65 (   12)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    5 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8579 (tm-30)
REVERT: H   23 LYS cc_start: 0.8480 (tppt) cc_final: 0.7917 (tptp)
REVERT: L  106 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8309 (pp)
REVERT: A  270 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8091 (pp)
REVERT: A  285 MET cc_start: 0.8957 (mtp) cc_final: 0.8700 (mtm)
REVERT: B  124 MET cc_start: 0.8511 (tpt) cc_final: 0.7969 (mmt)
REVERT: B  259 ASP cc_start: 0.8414 (t70) cc_final: 0.8156 (t0)
REVERT: B  390 LYS cc_start: 0.6582 (tmtt) cc_final: 0.6122 (mttm)
  outliers start: 24
  outliers final: 18
  residues processed: 144
  average time/residue: 0.1017
  time to fit residues: 20.0050
Evaluate side-chains
  138 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   30 SER
Chi-restraints excluded: chain L residue   31 ASN
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  423 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 91 optimal weight:    0.1980
   chunk 84 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  31 ASN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.135484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.108595 restraints weight = 11522.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.22
r_work: 0.3201 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8473  Z= 0.165
  Angle     :  0.639   7.853  11532  Z= 0.324
  Chirality :  0.046   0.286   1292
  Planarity :  0.004   0.049   1485
  Dihedral  :  5.128  31.078   1149
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 14.16 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.57 (0.24), residues: 1044
  helix: -3.05 (0.40), residues: 93
  sheet: -2.80 (0.25), residues: 359
  loop : -1.91 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  41 
 TYR   0.020   0.002   TYR A 288 
 PHE   0.013   0.001   PHE B 308 
 TRP   0.014   0.002   TRP A 235 
 HIS   0.007   0.001   HIS A 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.16 ( 8455)
  covalent geometry    : angle       0.63108 /  0.32 (11486)
  SS BOND              : bond        0.00516 /  0.26 (    8)
  SS BOND              : angle       0.97121 /  0.52 (   16)
  hydrogen bonds       : bond        0.03377 /  2.30 (  178)
  hydrogen bonds       : angle       7.55061 /  4.91 (  432)
  link_ALPHA1-3        : bond        0.01471 /  0.77 (    1)
  link_ALPHA1-3        : angle       1.95855 /  1.07 (    3)
  link_ALPHA1-4        : bond        0.01452 /  0.71 (    2)
  link_ALPHA1-4        : angle       2.46099 /  1.34 (    6)
  link_BETA1-4         : bond        0.00395 /  0.20 (    3)
  link_BETA1-4         : angle       1.20029 /  0.61 (    9)
  link_NAG-ASN         : bond        0.00460 /  0.22 (    4)
  link_NAG-ASN         : angle       2.24417 /  1.37 (   12)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: H    5 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8613 (tm-30)
REVERT: H   23 LYS cc_start: 0.8415 (tppt) cc_final: 0.7849 (tptp)
REVERT: L   39 LYS cc_start: 0.8488 (ptpt) cc_final: 0.8264 (mttt)
REVERT: L  106 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8321 (pp)
REVERT: A  208 ARG cc_start: 0.8332 (mmt-90) cc_final: 0.8017 (mmt-90)
REVERT: A  270 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7920 (pp)
REVERT: B  259 ASP cc_start: 0.8343 (t70) cc_final: 0.8037 (t0)
REVERT: B  390 LYS cc_start: 0.6589 (tmtt) cc_final: 0.6081 (mttm)
  outliers start: 30
  outliers final: 21
  residues processed: 145
  average time/residue: 0.0930
  time to fit residues: 18.4706
Evaluate side-chains
  150 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   98 ARG
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   30 SER
Chi-restraints excluded: chain L residue   31 ASN
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  215 HIS
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  423 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 95 optimal weight:    6.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  31 ASN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.135889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.108527 restraints weight = 11408.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.28
r_work: 0.3192 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8473  Z= 0.177
  Angle     :  0.637   8.257  11532  Z= 0.320
  Chirality :  0.046   0.370   1292
  Planarity :  0.004   0.049   1485
  Dihedral  :  5.041  30.893   1149
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.58 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.52 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.42 (0.25), residues: 1044
  helix: -2.89 (0.42), residues: 91
  sheet: -2.71 (0.25), residues: 369
  loop : -1.79 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  41 
 TYR   0.020   0.002   TYR A 288 
 PHE   0.013   0.001   PHE B 308 
 TRP   0.014   0.002   TRP H  47 
 HIS   0.007   0.001   HIS A 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00415 /  0.18 ( 8455)
  covalent geometry    : angle       0.62528 /  0.32 (11486)
  SS BOND              : bond        0.00348 /  0.23 (    8)
  SS BOND              : angle       0.86721 /  0.46 (   16)
  hydrogen bonds       : bond        0.03245 /  2.23 (  178)
  hydrogen bonds       : angle       7.34961 /  4.77 (  432)
  link_ALPHA1-3        : bond        0.01480 /  0.78 (    1)
  link_ALPHA1-3        : angle       1.96618 /  1.07 (    3)
  link_ALPHA1-4        : bond        0.01425 /  0.69 (    2)
  link_ALPHA1-4        : angle       2.41961 /  1.32 (    6)
  link_BETA1-4         : bond        0.00293 /  0.14 (    3)
  link_BETA1-4         : angle       0.99696 /  0.51 (    9)
  link_NAG-ASN         : bond        0.00444 /  0.21 (    4)
  link_NAG-ASN         : angle       3.15527 /  2.07 (   12)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
REVERT: H    5 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8610 (tt0)
REVERT: A  208 ARG cc_start: 0.8359 (mmt-90) cc_final: 0.8044 (mmt-90)
REVERT: A  270 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7974 (pp)
REVERT: A  285 MET cc_start: 0.8950 (mtm) cc_final: 0.8711 (mtm)
REVERT: B  124 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8020 (mmt)
REVERT: B  253 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8395 (mtmm)
REVERT: B  259 ASP cc_start: 0.8319 (t70) cc_final: 0.8044 (t0)
REVERT: B  390 LYS cc_start: 0.6581 (tmtt) cc_final: 0.6097 (mttm)
  outliers start: 28
  outliers final: 17
  residues processed: 149
  average time/residue: 0.0827
  time to fit residues: 16.7953
Evaluate side-chains
  144 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   31 ASN
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  215 HIS
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain B residue  253 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   chunk 92 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 102 optimal weight:    4.9990
   chunk 2 optimal weight:    0.0370
   overall best weight:    0.8660

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  31 ASN
L  38 GLN
** L  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 280 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.136218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.108829 restraints weight = 11385.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.28
r_work: 0.3196 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8473  Z= 0.175
  Angle     :  0.636   8.967  11532  Z= 0.319
  Chirality :  0.047   0.333   1292
  Planarity :  0.004   0.047   1485
  Dihedral  :  4.843  25.703   1147
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.58 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 16.97 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.38 (0.25), residues: 1044
  helix: -2.80 (0.42), residues: 91
  sheet: -2.67 (0.25), residues: 373
  loop : -1.77 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  84 
 TYR   0.021   0.002   TYR A 288 
 PHE   0.013   0.001   PHE B 308 
 TRP   0.014   0.001   TRP H  47 
 HIS   0.007   0.001   HIS A 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00408 /  0.17 ( 8455)
  covalent geometry    : angle       0.62411 /  0.32 (11486)
  SS BOND              : bond        0.00336 /  0.22 (    8)
  SS BOND              : angle       0.79882 /  0.42 (   16)
  hydrogen bonds       : bond        0.03119 /  2.15 (  178)
  hydrogen bonds       : angle       7.20697 /  4.68 (  432)
  link_ALPHA1-3        : bond        0.01414 /  0.74 (    1)
  link_ALPHA1-3        : angle       1.97443 /  1.08 (    3)
  link_ALPHA1-4        : bond        0.01418 /  0.69 (    2)
  link_ALPHA1-4        : angle       2.41853 /  1.32 (    6)
  link_BETA1-4         : bond        0.00302 /  0.15 (    3)
  link_BETA1-4         : angle       1.00477 /  0.53 (    9)
  link_NAG-ASN         : bond        0.00547 /  0.26 (    4)
  link_NAG-ASN         : angle       3.29254 /  2.16 (   12)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8601 (tpp) cc_final: 0.8322 (mmm)
REVERT: H   47 TRP cc_start: 0.8053 (OUTLIER) cc_final: 0.7614 (t60)
REVERT: L   39 LYS cc_start: 0.8548 (mttt) cc_final: 0.8269 (mttt)
REVERT: A  208 ARG cc_start: 0.8349 (mmt-90) cc_final: 0.8025 (mmt-90)
REVERT: A  270 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7810 (pp)
REVERT: B  124 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8003 (mmt)
REVERT: B  253 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8342 (mtmm)
REVERT: B  259 ASP cc_start: 0.8359 (t70) cc_final: 0.8076 (t0)
REVERT: B  390 LYS cc_start: 0.6533 (tmtt) cc_final: 0.6061 (mttm)
  outliers start: 30
  outliers final: 22
  residues processed: 154
  average time/residue: 0.0857
  time to fit residues: 18.2750
Evaluate side-chains
  154 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  215 HIS
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain B residue  253 LYS
Chi-restraints excluded: chain B residue  311 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 97 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9990
   chunk 99 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  38 GLN
** L  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.136143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.109082 restraints weight = 11465.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.23
r_work: 0.3201 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8473  Z= 0.186
  Angle     :  0.637   8.355  11532  Z= 0.320
  Chirality :  0.046   0.296   1292
  Planarity :  0.004   0.046   1485
  Dihedral  :  4.818  25.835   1147
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.87 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 18.31 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.29 (0.25), residues: 1044
  helix: -2.69 (0.42), residues: 91
  sheet: -2.59 (0.25), residues: 367
  loop : -1.75 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  41 
 TYR   0.021   0.002   TYR A 288 
 PHE   0.013   0.002   PHE A 171 
 TRP   0.015   0.001   TRP H  47 
 HIS   0.007   0.001   HIS A 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.19 ( 8455)
  covalent geometry    : angle       0.62638 /  0.32 (11486)
  SS BOND              : bond        0.00354 /  0.24 (    8)
  SS BOND              : angle       0.82719 /  0.44 (   16)
  hydrogen bonds       : bond        0.03103 /  2.15 (  178)
  hydrogen bonds       : angle       7.11850 /  4.62 (  432)
  link_ALPHA1-3        : bond        0.01371 /  0.72 (    1)
  link_ALPHA1-3        : angle       1.96621 /  1.07 (    3)
  link_ALPHA1-4        : bond        0.01544 /  0.75 (    2)
  link_ALPHA1-4        : angle       2.46339 /  1.36 (    6)
  link_BETA1-4         : bond        0.00322 /  0.16 (    3)
  link_BETA1-4         : angle       1.14180 /  0.57 (    9)
  link_NAG-ASN         : bond        0.00482 /  0.23 (    4)
  link_NAG-ASN         : angle       2.86230 /  1.82 (   12)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 0.239 
Fit side-chains
REVERT: H   34 MET cc_start: 0.8603 (tpp) cc_final: 0.8320 (mmm)
REVERT: H   47 TRP cc_start: 0.8011 (OUTLIER) cc_final: 0.7593 (t60)
REVERT: A  208 ARG cc_start: 0.8359 (mmt-90) cc_final: 0.8034 (mmt-90)
REVERT: A  270 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7839 (pp)
REVERT: B  124 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8003 (mmt)
REVERT: B  149 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8289 (pt)
REVERT: B  390 LYS cc_start: 0.6541 (tmtt) cc_final: 0.6055 (mttm)
  outliers start: 32
  outliers final: 24
  residues processed: 147
  average time/residue: 0.0783
  time to fit residues: 16.2640
Evaluate side-chains
  149 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   48 ILE
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  215 HIS
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  423 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 36 optimal weight:    0.0070
   chunk 87 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 101 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.5798

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  38 GLN
** L  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.138486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.111241 restraints weight = 11405.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.26
r_work: 0.3231 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8473  Z= 0.140
  Angle     :  0.626   9.440  11532  Z= 0.312
  Chirality :  0.046   0.342   1292
  Planarity :  0.004   0.046   1485
  Dihedral  :  4.727  26.242   1147
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 19.21 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.12 (0.25), residues: 1044
  helix: -2.55 (0.43), residues: 91
  sheet: -2.42 (0.26), residues: 341
  loop : -1.75 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  41 
 TYR   0.016   0.001   TYR A 288 
 PHE   0.010   0.001   PHE B 308 
 TRP   0.014   0.001   TRP H  47 
 HIS   0.006   0.001   HIS A 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 ( 8455)
  covalent geometry    : angle       0.60765 /  0.31 (11486)
  SS BOND              : bond        0.00263 /  0.17 (    8)
  SS BOND              : angle       0.68054 /  0.35 (   16)
  hydrogen bonds       : bond        0.03025 /  2.14 (  178)
  hydrogen bonds       : angle       6.92938 /  4.51 (  432)
  link_ALPHA1-3        : bond        0.01471 /  0.77 (    1)
  link_ALPHA1-3        : angle       2.11618 /  1.14 (    3)
  link_ALPHA1-4        : bond        0.01479 /  0.72 (    2)
  link_ALPHA1-4        : angle       2.59191 /  1.45 (    6)
  link_BETA1-4         : bond        0.00316 /  0.16 (    3)
  link_BETA1-4         : angle       1.42674 /  0.75 (    9)
  link_NAG-ASN         : bond        0.00627 /  0.30 (    4)
  link_NAG-ASN         : angle       4.00076 /  2.55 (   12)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 137
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   10 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8136 (mm-30)
REVERT: H   34 MET cc_start: 0.8588 (tpp) cc_final: 0.8295 (mmm)
REVERT: H   47 TRP cc_start: 0.7990 (OUTLIER) cc_final: 0.7558 (t60)
REVERT: L   61 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7754 (mtm-85)
REVERT: A  208 ARG cc_start: 0.8383 (mmt-90) cc_final: 0.8079 (mmt-90)
REVERT: A  285 MET cc_start: 0.8989 (mtm) cc_final: 0.8756 (ttm)
REVERT: B  124 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7934 (mmt)
REVERT: B  149 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8257 (pt)
REVERT: B  390 LYS cc_start: 0.6612 (tmtt) cc_final: 0.6130 (mttm)
  outliers start: 29
  outliers final: 20
  residues processed: 152
  average time/residue: 0.0726
  time to fit residues: 15.6401
Evaluate side-chains
  150 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  215 HIS
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  423 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0980
   chunk 101 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 94 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0970
   overall best weight:    0.5378

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  54 ASN
L  38 GLN
L  92 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.138330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.111218 restraints weight = 11351.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.29
r_work: 0.3236 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8473  Z= 0.135
  Angle     :  0.618   9.546  11532  Z= 0.309
  Chirality :  0.045   0.332   1292
  Planarity :  0.004   0.048   1485
  Dihedral  :  4.651  26.233   1147
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.11 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.95 (0.25), residues: 1044
  helix: -2.33 (0.44), residues: 88
  sheet: -2.31 (0.27), residues: 339
  loop : -1.67 (0.25), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  41 
 TYR   0.013   0.001   TYR A 288 
 PHE   0.010   0.001   PHE B 308 
 TRP   0.014   0.001   TRP H  47 
 HIS   0.006   0.001   HIS A 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.13 ( 8455)
  covalent geometry    : angle       0.60248 /  0.31 (11486)
  SS BOND              : bond        0.00251 /  0.16 (    8)
  SS BOND              : angle       0.70962 /  0.36 (   16)
  hydrogen bonds       : bond        0.02908 /  2.10 (  178)
  hydrogen bonds       : angle       6.82324 /  4.43 (  432)
  link_ALPHA1-3        : bond        0.01512 /  0.80 (    1)
  link_ALPHA1-3        : angle       2.17257 /  1.18 (    3)
  link_ALPHA1-4        : bond        0.01454 /  0.71 (    2)
  link_ALPHA1-4        : angle       2.47272 /  1.36 (    6)
  link_BETA1-4         : bond        0.00395 /  0.20 (    3)
  link_BETA1-4         : angle       1.01355 /  0.52 (    9)
  link_NAG-ASN         : bond        0.00476 /  0.23 (    4)
  link_NAG-ASN         : angle       3.73500 /  2.32 (   12)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8563 (tpp) cc_final: 0.8269 (mmm)
REVERT: H   47 TRP cc_start: 0.7961 (OUTLIER) cc_final: 0.7577 (t60)
REVERT: L   61 ARG cc_start: 0.8226 (mtm-85) cc_final: 0.7749 (mtm-85)
REVERT: A  208 ARG cc_start: 0.8400 (mmt-90) cc_final: 0.8090 (mmt-90)
REVERT: A  259 THR cc_start: 0.9104 (m) cc_final: 0.8744 (p)
REVERT: A  285 MET cc_start: 0.8992 (mtm) cc_final: 0.8757 (ttm)
REVERT: B  124 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7874 (mmt)
REVERT: B  149 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8227 (pt)
REVERT: B  390 LYS cc_start: 0.6706 (tmtt) cc_final: 0.6243 (mttm)
  outliers start: 26
  outliers final: 22
  residues processed: 145
  average time/residue: 0.0810
  time to fit residues: 16.6326
Evaluate side-chains
  150 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  215 HIS
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  423 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 94 optimal weight:    0.0770
   chunk 77 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 25 optimal weight:    0.4980
   chunk 99 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.6740

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.137880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.111011 restraints weight = 11301.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.23
r_work: 0.3240 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8473  Z= 0.149
  Angle     :  0.626   8.996  11532  Z= 0.312
  Chirality :  0.046   0.322   1292
  Planarity :  0.004   0.047   1485
  Dihedral  :  4.652  26.122   1147
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 20.45 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.99 (0.25), residues: 1044
  helix: -2.44 (0.43), residues: 91
  sheet: -2.34 (0.26), residues: 343
  loop : -1.66 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  41 
 TYR   0.013   0.001   TYR L  71 
 PHE   0.012   0.001   PHE B 308 
 TRP   0.015   0.001   TRP H  47 
 HIS   0.006   0.001   HIS A 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 ( 8455)
  covalent geometry    : angle       0.61249 /  0.31 (11486)
  SS BOND              : bond        0.00298 /  0.19 (    8)
  SS BOND              : angle       0.72172 /  0.37 (   16)
  hydrogen bonds       : bond        0.02983 /  2.15 (  178)
  hydrogen bonds       : angle       6.79626 /  4.42 (  432)
  link_ALPHA1-3        : bond        0.01503 /  0.79 (    1)
  link_ALPHA1-3        : angle       2.16373 /  1.17 (    3)
  link_ALPHA1-4        : bond        0.01461 /  0.71 (    2)
  link_ALPHA1-4        : angle       2.47003 /  1.36 (    6)
  link_BETA1-4         : bond        0.00343 /  0.17 (    3)
  link_BETA1-4         : angle       0.98409 /  0.51 (    9)
  link_NAG-ASN         : bond        0.00455 /  0.22 (    4)
  link_NAG-ASN         : angle       3.52506 /  2.19 (   12)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2088 Ramachandran restraints generated.
    1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   10 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8026 (mm-30)
REVERT: H   34 MET cc_start: 0.8574 (tpp) cc_final: 0.8280 (mmm)
REVERT: H   47 TRP cc_start: 0.7939 (OUTLIER) cc_final: 0.7580 (t60)
REVERT: L   61 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7727 (mtm-85)
REVERT: A  259 THR cc_start: 0.9122 (m) cc_final: 0.8733 (p)
REVERT: A  285 MET cc_start: 0.8992 (mtm) cc_final: 0.8734 (ttm)
REVERT: B  124 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7821 (mmt)
REVERT: B  149 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8184 (pt)
REVERT: B  343 LEU cc_start: 0.8558 (tt) cc_final: 0.8344 (tt)
REVERT: B  390 LYS cc_start: 0.6677 (tmtt) cc_final: 0.6212 (mttm)
  outliers start: 27
  outliers final: 22
  residues processed: 144
  average time/residue: 0.0764
  time to fit residues: 15.2916
Evaluate side-chains
  151 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   27 TYR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue   92 ASN
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  144 SER
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  215 HIS
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  124 MET
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  423 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 82 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 91 optimal weight:    0.3980
   chunk 22 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 60 optimal weight:    0.7980
   chunk 76 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.138181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.111356 restraints weight = 11351.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 2.24
r_work: 0.3249 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8473  Z= 0.141
  Angle     :  0.624  10.440  11532  Z= 0.309
  Chirality :  0.045   0.311   1292
  Planarity :  0.004   0.046   1485
  Dihedral  :  4.602  26.190   1147
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.67 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.91 (0.25), residues: 1044
  helix: -2.17 (0.45), residues: 88
  sheet: -2.31 (0.26), residues: 343
  loop : -1.62 (0.25), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  41 
 TYR   0.013   0.001   TYR L  71 
 PHE   0.011   0.001   PHE B 308 
 TRP   0.015   0.001   TRP H  47 
 HIS   0.006   0.001   HIS A 338 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.14 ( 8455)
  covalent geometry    : angle       0.61138 /  0.31 (11486)
  SS BOND              : bond        0.00281 /  0.18 (    8)
  SS BOND              : angle       0.76261 /  0.39 (   16)
  hydrogen bonds       : bond        0.02880 /  2.10 (  178)
  hydrogen bonds       : angle       6.76926 /  4.40 (  432)
  link_ALPHA1-3        : bond        0.01528 /  0.80 (    1)
  link_ALPHA1-3        : angle       2.19947 /  1.19 (    3)
  link_ALPHA1-4        : bond        0.01433 /  0.70 (    2)
  link_ALPHA1-4        : angle       2.43994 /  1.34 (    6)
  link_BETA1-4         : bond        0.00347 /  0.17 (    3)
  link_BETA1-4         : angle       0.96166 /  0.49 (    9)
  link_NAG-ASN         : bond        0.00456 /  0.22 (    4)
  link_NAG-ASN         : angle       3.33634 /  2.07 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2114.09 seconds
wall clock time: 36 minutes 57.34 seconds (2217.34 seconds total)